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Where the money is: The last mystery in MTA finances is a contract for transit workers, like these doing construction at the Brooklyn Bridge station. Photo: Christopher Sadowski

Where the money is: The last mystery in MTA finances is a contract for transit workers, like these doing construction at the Brooklyn Bridge station. (Christopher Sadowski)

Gov. Cuomo is getting his back slapped this week for a budget deal well-done. But on one topic — the state-run MTA — the governor deserves an “incomplete,” at best. In key ways, the budget deal actually makes the MTA’s woes worse.

The big worry was that Albany wouldn’t find the $13.1 billion that the MTA needs over three years to keep the system in decent shape — to do such things as buy subway cars to replace 50-year-old cars on the C line, and work on the new Second Avenue stations so the line can open in four years.

On that front, the governor has saved the day. But saving the day will cost big in future years. Of that $13.1 billion, only $770 million — less than 6 percent — will come in cash. Then, the state assumes the feds will give us some money.

Where will Cuomo get the rest? New debt. The deal lets the MTA borrow an extra $7 billion, more than half of what Cuomo called “full funding” for the MTA’s investments

The debt binge, along with borrowing done these last two years, will bring the MTA’s total debt up by 37 percent from 2010 to 2017, to $41 billion.

All this debt has to be repaid — or, at least, the interest has to be paid. Half a decade from now, the MTA will be spending more than $3.3 billion a year just to stay above this burden, up more than 64 percent from today.

Merely keeping up with these debt payments will cost the MTA nearly a quarter of all its receipts from fares, tolls and taxes — up from 16 percent right now.

So fares, tolls and taxes will go up — just as they have in the last three years. Fares were already set to rise 7.5 percent next year, beyond inflation (probably). But the new debt means fare hikes down the line will be worse.

Just because Cuomo may be out of office by then doesn’t mean they won’t be his hikes, just as the last few jumps were former Gov. George Pataki’s fault.

But even that pain may not solve the problem. After all, when the pols created a $1.5 billion-a-year tax on workers in downstate New York back in 2009, it was supposed to bail out the MTA once and forever.

Uh-uh. This week, the MTA said revenues from the payroll tax are coming in 13 percent below budget this month, “likely the result of lower annual bonuses” on Wall Street. (The tax hits everyone’s pay, including bonuses.)

There is one way that Cuomo can ease the pain: Get more bang for the MTA’s labor buck. Now is the time, because the MTA’s contract with the Transport Workers Union expired nearly three months ago.

So far, the signs aren’t great. Cuomo has been more than friendly to the TWU. His “sweeping pension reform,” for example, wasn’t so sweeping for transit.

As union officials gloat, “while nearly every other union . . . had their retirement age pushed back to 63, we were successful” in keeping a retirement age of 55 after 25 years’ worth of work. Nor did the TWU have to pay anything extra to make up for this privilege.

All this makes it even more important that union workers don’t get much in raises in their new contract — unless they pay for them with big changes to work rules (which can force the MTA to pay people to stand or sit around) and to the health-care plan, so that the public can save on those costs.

Yet all is quiet. The union is still adamant that it wants cost-of-living raises, plus extra for work-rule changes, and it wants its health plan improved.

MTA chief Joe Lhota and union head John Samuelson don’t let these trifles get in the way of their good relations. “They attend stuff together,” says one observer.

Lawmakers aren’t helping, either. Brooklyn state Sen. Marty Golden, a Republican, last week, opined publicly in Albany that “three zeroes” instead of raises “doesn’t really work well, especially if you live in the New York City area.”

That’s a big help to Lhota if he wants to hold the line — and help Cuomo keep the trains from running off the rails.

Nicole Gelinas is a contributing editor to the Manhattan Institute’s City Journal.